rs2524068

chr6-31277284-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000494673.1(USP8P1):n.1713G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 794,154 control chromosomes in the GnomAD database, including 10,284 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.17 (2256 hom., cov: 32)
  • Exomes 𝑓: 0.15 (8028 hom.)
• Consequence: USP8P1 ENST00000494673.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.866

Genes affected

USP8P1 (HGNC:13987): (USP8 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
USP8P1	ENST00000494673.1	n.1713G>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25774 AN: 152056 Hom.: 2252 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.175

GnomAD4 exome AF: 0.152 AC: 97364 AN: 641978 Hom.: 8028 Cov.: 6 AF XY: 0.146 AC XY: 51047 AN XY: 348452

Gnomad4 AFR exome AF: 0.193

Gnomad4 AMR exome AF: 0.162

Gnomad4 ASJ exome AF: 0.176

Gnomad4 EAS exome AF: 0.104

Gnomad4 SAS exome AF: 0.0676

Gnomad4 FIN exome AF: 0.114

Gnomad4 NFE exome AF: 0.172

Gnomad4 OTH exome AF: 0.173

GnomAD4 genome AF: 0.170 AC: 25795 AN: 152176 Hom.: 2256 Cov.: 32 AF XY: 0.164 AC XY: 12219 AN XY: 74398

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.100

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.176

Alfa AF: 0.171 Hom.: 1405

Bravo AF: 0.177

Asia WGS AF: 0.141 AC: 491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
Cadd	Benign	7.5
Dann	Benign	0.77

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2524068; hg19: chr6-31245061;